When and why did the designer put bacterial DNA into our genome?

[RonO]

http://www.the-scientist.com/?articles.view/articleNo/47125/title/Bacteria-and-Humans-Have-Been-Swapping-DNA-for-Millennia/

Our lineage may not have been swapping much DNA with bacteria for a
while in terms of our germline. When our ancestors (single cell
ancestors) first acquired the bacterial endosymbiont that became our
mitochondria there was a lot of gene transfer from the endosymbiont
bacteria and the host for our lineage. Other lineages did not transfer
as much DNA from the bacteria into the host and their mitochondrial
genomes still contain quite a few genes. For some reason our lineage
transferred just about everything and left only the translation RNA
machinery (rRNAs and tRNAs) and 13 protein genes in the mitochondrial
genome. The rest of the oxidative phosphorylation genes were
transferred to the nucleus, and whatever else we found that was useful
that came from the endosymbiont.

There were likely DNA transfers before this, and likely after, but
humans as a species hasn't done much of it in the last million years.
We are getting a lot of genomic sequence and can tell the parts that
came from bacteria, and they aren't finding much that was transferred
recently.

A lot of bacteria can pick up DNA from the environment and incorporate
it into their genomes, and we have evidence of recent transfers, but for
us the DNA has to be transferred into cells that become the germline
that produces sperm and eggs. My guess is that our gut cells have the
highest probability for incorporating bacterial DNA, but unless we clone
a human from such cells you won't see a human wandering around with that
bacterial DNA in their germcells. It looks like some researchers are
finding evidence of recent transfer of bacterial DNA in human tumor
cells. These cells acquire the DNA and because the cancer amplifies
that cell we can get a lot of copies of that genome and confirm that
there is new bacterial DNA in it. This DNA may even have something to
do with causing the cancer. Time will tell, but it looks like we still
have the ability to acquire foreign DNA even if it is rare to get it
into germline cells.

IDiots have to try to figure out when, where and why the designer did
these kinds of transfers in the ancient past in order to create some
type of equivalent alternative. Maybe they happened when the designer
wasn't looking. How can you tell? Is the designer putting the
bacterial DNA into the tumor cells?

Ron Okimoto

[solar penguin]

On Sunday, 16 October 2016 17:05:03 UTC+1, Ron O wrote:

>
> IDiots have to try to figure out when, where and why the designer did
> these kinds of transfers in the ancient past in order to create some
> type of equivalent alternative. Maybe they happened when the designer
> wasn't looking. How can you tell? Is the designer putting the
> bacterial DNA into the tumor cells?
>

I know this is probably a stupid question, but how do you _know_ it's real
bacteria DNA? There are only so many ways to arrange sequences using only
four different symbols. By the law of averages, you're bound to find some
sequences the same in different lifeforms just by coincidence.

Yeah, yeah, in the ordinary, everyday world coincidences don't really
explain anything, so they're always the last resort, held back for when all
other explanations have failed. But in the crazy topsy-turvy world of
science, it's the other way round. Coincidences are always the default
explanation to be used until there's very strong evidence otherwise.
(e.g. "No, you don't have psychic powers! The results were just a
coincidence!)

So, what is the very strong evidence that this DNA really did come from a
bacteria? OTOH since you also say bacteria steal DNA from humans, how do
you know it didn't come from humans in the first place. (After all, the
genetic code doesn't say plain things like "Be a bacterium, not a human!"
so it must be hard to tell what it actually is.)

(BTW there's also a very nasty ethical question: If cancer patients have a
higher proportion of bacteria DNA, does that mean they're less human and so
should treatment be denied to them? That's a frightening thought!)

[RonO]

On 10/17/2016 4:04 AM, solar penguin wrote:
> On Sunday, 16 October 2016 17:05:03 UTC+1, Ron O wrote:
>
>>
>> IDiots have to try to figure out when, where and why the designer did
>> these kinds of transfers in the ancient past in order to create some
>> type of equivalent alternative. Maybe they happened when the designer
>> wasn't looking. How can you tell? Is the designer putting the
>> bacterial DNA into the tumor cells?
>>
>
> I know this is probably a stupid question, but how do you _know_ it's real
> bacteria DNA? There are only so many ways to arrange sequences using only
> four different symbols. By the law of averages, you're bound to find some
> sequences the same in different lifeforms just by coincidence.
>
> Yeah, yeah, in the ordinary, everyday world coincidences don't really
> explain anything, so they're always the last resort, held back for when all
> other explanations have failed. But in the crazy topsy-turvy world of
> science, it's the other way round. Coincidences are always the default
> explanation to be used until there's very strong evidence otherwise.
> (e.g. "No, you don't have psychic powers! The results were just a
> coincidence!)
>
> So, what is the very strong evidence that this DNA really did come from a
> bacteria? OTOH since you also say bacteria steal DNA from humans, how do
> you know it didn't come from humans in the first place. (After all, the
> genetic code doesn't say plain things like "Be a bacterium, not a human!"
> so it must be hard to tell what it actually is.)

It is usually whole genes that are left intact or they wouldn't have
been selected for to be maintained in the population. Random bits could
be fixed by drift, but if after millions of years the gene is intact it
is likely selection.

When you have the whole gene you can compare it to other closely related
species and to bacteria. In the case of the article they could identify
the bacteria that the gene came from.

There may be a limited number of ways that you can arrange a sequence,
but use the creationist probability argument and you would soon see that
doing such a thing by purely random chance would be pretty much
impossible. It isn't due to random chance. The genes evolved in
bacteria, and they got transferred to other organisms and they have been
passed down by descent with modification and natural selection.

>
> (BTW there's also a very nasty ethical question: If cancer patients have a
> higher proportion of bacteria DNA, does that mean they're less human and so
> should treatment be denied to them? That's a frightening thought!)
>

There is no such ethical argument here. It is the tumor cells that has
more bacterial DNA than the host. No one that I know of thinks that
cancer has a right to life. You could be the first to start such a
movement and see how far it gets. I'd start with the Hindus and
Buddhists. Start claiming that their lost relatives could be tumor
cells that need to be preserved. Some of these lost relatives would
have been known to be leaches and cancers in the family so it might make
sense. Just think what would become of the research that creates all
those tumors in rats and mice.

Ron Okimoto

[jillery]

Another point is that most genes are thousands of nucleotides long. So
even with only 4 nucleotides, to get that specific order by chance is
very unlikely. By analogy, toss a coin a thousand times, just heads
or tails. The probability of matching that 1000-toss sequence by
random chance is 1 in 2^1000.

>> (BTW there's also a very nasty ethical question: If cancer patients have a
>> higher proportion of bacteria DNA, does that mean they're less human and so
>> should treatment be denied to them? That's a frightening thought!)
>>
>
>There is no such ethical argument here. It is the tumor cells that has
>more bacterial DNA than the host. No one that I know of thinks that
>cancer has a right to life. You could be the first to start such a
>movement and see how far it gets. I'd start with the Hindus and
>Buddhists. Start claiming that their lost relatives could be tumor
>cells that need to be preserved. Some of these lost relatives would
>have been known to be leaches and cancers in the family so it might make
>sense. Just think what would become of the research that creates all
>those tumors in rats and mice.
>
>Ron Okimoto

--
This space is intentionally not blank.

[solar penguin]

Thanks Ron and Jillery for answering that. (Creationists, see, that's how
to answer questions!)

There's just one little thing I'm not sure about. AIUI genes code for things
like, "Make this amount of this chemical", or "that amount of that chemical",
not "be bacteria" or "be human". Even if we do have the same genes, could it
just be because human cells and bacterial cells need the same chemicals and
so had to independently evolve the same genes to make them?

[Bill Rogers]

You could say that genes code for enzymes which catalyze some biochemical reaction. Take some reaction as an example, say, cleavage of a phosphodiester bond. We do it, plants do it, bacteria do it. But there are many different phosphodiesterases in the world (and therefore many different genes with different sequences that code for the phosphodiesterases) that can do the job. So the constraints on the evolution of a phosphodiesterase are nowhere near strict enough to require that bacteria and humans evolve identical sequences to do the job.

Apart from that there are other, more generic differences between human and bacterial genes that suggest the bacterial genes transferred to humans really came from bacteria. The codon usage and G-C content are different, and bacterial genes, as a rule, do not have introns, while human genes generally do.

The main problem with identifying bacterial genes transferred into human genomes is the technical problem of being sure that the bacterial DNA was not a contaminant in the human DNA prep being used for the human sequencing. There are sequencing technologies for which it is possible to produce artifactual hybrid human-bacterial sequences that look like they are part of the human genome. People working in this area are well aware of that potential error, though, and take careful steps to rule it out.

[RonO]

It doesn't matter in terms of origin of the gene. It can do the same
thing in both organisms, but may have evolved in one or the other. In
the cases that we are talking about the genes obviously evolved in
bacteria and were recently transferred to the human tumor cells. The
non tumor cells from the same individuals do not have the new bacterial
DNA, and other humans do not have the new bacterial DNA. They can go to
the data base and match up what bacteria the DNA came from.

When our ancestors picked up bacteria as endosymbionts and DNA from the
bacteria that became our mitochondria was transferred to the nucleus of
the host they did the same thing. Some of the gene products are even
translocated back into the mitochondria in order for them to do their
normal functions.

We might have evolved all of these genes independently, but we obviously
did not have to because bacteria had already evolved the genes. We have
no evidence that our eukaryotic ancestors could perform oxidative
phosphorylation before we acquired the bacteria that could do it. We
can tell that the mitochondrial DNA is bacterial in origin because of
the sequence relationships of the genes that still exist. The
mitochondrial ribosomal genes are most closely related to bacteria
(purple sulfur bacteria). They work in translation, just like our
ribosomal genes that we inherited more directly from our eukaryotic
ancestor, so why would they have to evolve independently to be more like
purple sulfur bacteria? Since we know that the DNA transfer can occur
it isn't much of a stretch to conclude that the DNA came from bacteria.

We obviously can evolve genes that do the same things that genes in
bacteria do, but they would not look like they came from a certain
bacteria. They would have a different evolutionary history. We can
tell that by looking at the sequence.

Ron Okimoto

[eridanus]

you have to read the genesis to answer this question.
eri

[solar penguin]

Yeah, I guess that makes sense. Thanks guys.

TBH I'll never by totally convinced by the idea that scientists can tell a
gene's evolutionary history just by looking at it. (Reading a published novel
doesn't tell you what the first draft was like!) But this does seem to be one
of those special exceptions where circumstances do allow scientists to get it
right. So, yeah, thanks for explaining it.

[eridanus]

El domingo, 16 de octubre de 2016, 17:05:03 (UTC+1), Ron O escribió:

god almighty was one day bored, and he started to play games with the genes
of people and bacterias. "I would give atheist reasons to be unbelievers"
was god saying.

eri

[RonO]

A book isn't a very good example, neither is computer code. The fact is
that we can tell the origin of a sequence and given enough endpoints
(existing species) we can work backwards and estimate what the ancestral
sequence was for all those species. Eddie put up the example of the
estrogen receptors. You have a lot of estrogen receptors in your genome
and they evolved from a common ancestral estrogen receptor by gene
duplication. Sometime in the past one estrogen receptor diverged to
identify other ligands like androgens. By looking at the extant
sequence and working backwards researchers are able to figure out what
the ancestral sequences looked like.

Take a sequence AATAATAATAAT
Say that you have 6 extant species that share a common ancestor and when
you look at their sequences you find:

TATAATAATAAT
AATGATAATAAT
AATAATATTAAT
ACTAATAATAAT
AATAATAATAAA
AACAATAATAAT

AATAATAATAAT would be the ancestral sequence.

When you get stretches like this for hundreds or thousands of
nucleotides you can tell what the ancestral sequences is by looking at
how the extant sequences compare to each other. In this simplified case
each sequence varies by two positions from each other, but the rest of
the sequence is the same. They all vary by one substitution from the
ancestral sequence. By making all pairwise combinations you can
determine the most likely nucleotide that was in the ancestral sequence
that all 6 evolved from. It is more complex than this because we have
to deal with the fact that some mutations are more likely to occur than
others, and that there is lineage sorting of variation segregating in
any population that speciates. It is good if you have an outgroup (one
species that shares a common ancestor with all the other taxa in your
study). A monkey would be an outgroup if you were looking at all apes
including humans. It works even better if you have a bunch of monkeys
species to nail down the sequence changes that occurred in that lineage
and a bunch of apes. As you see in the example above the more species
that you have the more branch points that you cover and you can more
accurately determine the ancestral sequence.

For the chimp human example our sequence differs from a chimp by 1 in a
hundred base-pairs. It is easy to identify the related sequences in
such closely related species. Bacterial DNA has no such sequence
similarity. Even genes that share common ancestors are so different by
now that you can't mix them up. You won't find them in humans, chimps
or gorillas, and if such a sequence showed up like it does in the tumor
cells, and you can look in the database and see that it came from a
certain type of bacteria what would you conclude happened?

Ron Okimoto

Ron Okimoto

[solar penguin]

On Saturday, 22 October 2016 12:25:02 UTC+1, Ron O wrote:

> On 10/22/2016 2:30 AM, solar penguin wrote:

> >
> > Yeah, I guess that makes sense. Thanks guys.
> >
> > TBH I'll never by totally convinced by the idea that scientists can tell a
> > gene's evolutionary history just by looking at it. (Reading a published
> > novel doesn't tell you what the first draft was like!) But this does seem
> > to be one of those special exceptions where circumstances do allow
> > scientists to get it right. So, yeah, thanks for explaining it.
> >
>
> A book isn't a very good example, neither is computer code.

OK, but you'll have to put up with the book metaphor for a little bit longer.
Sorry. I'm afraid I'm one of those people who finds it easier to think in
terms of metaphor and allusionrather than direct facts.

And if I understand what you're saying below, the process works because if the
genome is like a book, it's not a finished, published novel but an author's
handwritten notebook where the story is still in the process of being written.
There are lots of crossed out sections that we can still read, whole passages
rewritten with changes, notes scribbled in the margins of earlier pages, etc.

(And before any Creationists try taking this post out of context, I'm not
suggesting the "author" is anything more than a useful metaphor!)

Is this right? Is that what you're saying lets the scientists reconstruct the
history of the earliest drafts? (If so, you could've said so, instead of
making me waste my time struggling through all the scientific technobabble!)

[RonO]

On 10/22/2016 7:16 AM, solar penguin wrote:
> On Saturday, 22 October 2016 12:25:02 UTC+1, Ron O wrote:
>
>> On 10/22/2016 2:30 AM, solar penguin wrote:
>
>>>
>>> Yeah, I guess that makes sense. Thanks guys.
>>>
>>> TBH I'll never by totally convinced by the idea that scientists can tell a
>>> gene's evolutionary history just by looking at it. (Reading a published
>>> novel doesn't tell you what the first draft was like!) But this does seem
>>> to be one of those special exceptions where circumstances do allow
>>> scientists to get it right. So, yeah, thanks for explaining it.
>>>
>>
>> A book isn't a very good example, neither is computer code.
>
> OK, but you'll have to put up with the book metaphor for a little bit longer.
> Sorry. I'm afraid I'm one of those people who finds it easier to think in
> terms of metaphor and allusionrather than direct facts.
>
> And if I understand what you're saying below, the process works because if the
> genome is like a book, it's not a finished, published novel but an author's
> handwritten notebook where the story is still in the process of being written.
> There are lots of crossed out sections that we can still read, whole passages
> rewritten with changes, notes scribbled in the margins of earlier pages, etc.
>
> (And before any Creationists try taking this post out of context, I'm not
> suggesting the "author" is anything more than a useful metaphor!)
>
> Is this right? Is that what you're saying lets the scientists reconstruct the
> history of the earliest drafts? (If so, you could've said so, instead of
> making me waste my time struggling through all the scientific technobabble!)

It is just something that you will have to deal with. A book metaphor
is bad and doesn't match up much with what happens with the evolution of
biological genetic material. This is just fact. You are just going to
have to deal with what is.

The closest thing like biological evolution among books is when they
were hand written before printing presses. The books were copied by
scribes, my guess is that some of them didn't even understand the
languages that they were copying. Mistakes were made in copying. If
they weren't so bad that anyone copying them would not correct them they
got passed the next scribe and this scribe added his own errors. The
errors would build into a lineage and you had a good date for when some
of the books in the lineage were copied you could put other "copies"
into this lineage by what errors they contained and when these errors
occurred. In effect you know what copies came from what previous copies.

For a really popular book you will get branching lineages of errors.
Some people get to copy the original, but others are stuck copying the
5th or 6th generation. The original might be lost and what you get
stuck with are copies of copies, but if you have enough extant copies
you can put the errors into a phylogeny and determine that one extant
book came from a certain fifth generation copy that is shared by another
extant book, but that had it's own copy history and may have contained
some other errors but that also contained all the errors in the same
fifth generation copy. There may have been hundreds of fifth generation
copies, but those two extant books would be determined to share the same
fifth generation ancestor due to the unique errors that some scribe put
into it and it would also have all the errors of the previous generation.

To make it simple say we just took the first 10 pages of the book. One
scribe copies the original book and makes an error on page 1. Another
scribe copies the same original but makes an error on page 2 and 3.
Another scribe gets copy one and makes an error on page 4 (1,4), and
someone copies copy 2 and makes an error on page 5 (2, 3, 5). The
second copy for copy 1 gets an error on page 10 (1, 4, 10). The second
lineage adds an error on page 6 for that generation (2, 3, 5, 6). In
biology we only have the extant lineages (latest copies), but in this
example you have all the copies and you know the order that they were
created. You can compare them all and recreate the original and fix all
the errors, and you can determine without knowing the order before hand
that copy 1 for one lineage had the error on page one, the error on page
4 came next and the last error was on page 10. The lineage was (1), (1,
4), (1, 4, 10). You just make the determination by the minimum number
of changes you have to make to create that order. You can do the same
thing for the second lineage from the original. (2, 3), (2, 3, 5), (2,
3, 5, 6).

Taking all the copies and looking at the errors you know that you are
dealing with 2 separate lineages of copy errors.

(1), (1, 4), (1, 4, 10)
and
(2, 3), (2, 3, 5), (2, 3, 5, 6)

Two different scribes copy a third generation book and create their own
errors and the lineage splits into two from (1, 4, 10)

(1, 4, 7, 10)
and
(1, 4, 8, 10)


more errors in newer copies and the lineage gets extended

(1, 4, 5b, 7, 10)
and
(1, 4, 8, 9, 10)

b. not the same error on page 5 as lineage (2, 3, 5, 6).

You know how books are copied by hand and you know that they copy a
previously existing copy, so even if you are missing some of the
intermediates you still know what lineage the copies most likely belong
to and when they split off.

So say that these two lineages are well established because the third
generation copies have been copied multiple times and we have hundreds
of examples where the two lineages are confirmed.

You find find a book where the first three pages have been swapped out.
(1, 4, 8, 9, 10) and (2, 3, 5, 6)

(2, 3, 4, 8, 9, 10). So you have a chimeria of two well established
lineages and it seems that some scribe had a copy of lineage 1, but it
was missing the first 3 pages so he obtained a copy of lineage 2 and put
in the missing pages.

When we see horizontal transfer from bacteria we are not just talking
about a couple errors on a few pages. We are talking about genes
thousands of base-pairs long that may have less than 30% sequence
similarity to anything in the recipient showing up where they shouldn't
be when we know that they are found in bacteria. It isn't guessing. If
you have the actual bacteria that the DNA came from it isn't even
questionable where the sequence came from.

Ron Okimoto

[jillery]

I have thought of the differences between your analogy above, of a
series of inaccurate transcriptions from multiple scribes, and solar
penguin's analogy, of a series of editions from a single author. Apart
from that, I confess I fail to recognize a substantial difference, and
ISTM both illustrate more or less equally well the concept of using
gene sequences to document historical genetic relationships among
species.

In the past, at least one poster described a good analogy of multiple
generations of copies from a poorly maintained copying machine.

OTOH ISTM Solar penguin's statement, that the latest edition doesn't
show what the first edition looks like, is technically correct but
misses the point, that it takes a several examples to identify those
relationships.

[RonO]

Penguin's analogy is more like horizontal transfer and does not
necessarily amount to the same thing as successive edits.

As you indicate you do not just need a linear progression of edited
manuscripts. In my example, just like in nature, you can take all the
extant copies and infer the phylogenetic relationships. Penguin will
not have that. My book example isn't the same as nature because we have
early editions and not just extant species. We would need to identify
the youngest copies of the hand written books and work backwards. It is
like having fossil DNA of extinct species, but we don't know which books
are the fossils.

Ron Okimoto

[jillery]

You claim that Solar Penguin's analogy is poorer because it allows
something equivalent to HGT. IIUC that's because authors can add to
new editions text from random sources. I submit that your analogy's
scribes also likely added without annotation de novo apologetics to
their copies. Plus, old editions hang around despite the appearance
of newer ones.

I understood both of these analogies to claim earlier editions and
earlier copies as analogous to living species. If instead I consider
earlier works as analogous to extinct species, then ISTM both
analogies are equally poor in that regard. Do you mean your analogy
to consider only the latest copy? If so, then what other examples
would you have to compare to it?

[RonO]

It wasn't just this point it was the fact that his evolution was linear.
He did not have branching that is required to use extant sequences to
infer the ancestral.

>
> I understood both of these analogies to claim earlier editions and
> earlier copies as analogous to living species. If instead I consider
> earlier works as analogous to extinct species, then ISTM both
> analogies are equally poor in that regard. Do you mean your analogy
> to consider only the latest copy? If so, then what other examples
> would you have to compare to it?

No, because there is branching in my example as different copiers copy
the same text and others copy their copies.

I told you why my analogy fails because we don't know the fossils from
the extant text. If we get enough samples we can infer some of the
fossils, but in effect all the books are their own endpoints, they are
all dead extinct populations that have not changed since they became
extinct (the copy was finished).

The older copies are equivalent to the fossil DNA of extinct species
that we are getting information from. Not only is the older edition a
fossil but it can be the missing link the actual ancestral species that
we are unlikely to find in the fossil record.

Ron Okimoto

[jillery]

On the one hand, there are authors who work on multiple versions of
their books. OTOH I agree Solar Penguin's analogy described published
editions, which infer a sequential lineage, and that makes it a weaker
analogy.

>I told you why my analogy fails because we don't know the fossils from
>the extant text. If we get enough samples we can infer some of the
>fossils, but in effect all the books are their own endpoints, they are
>all dead extinct populations that have not changed since they became
>extinct (the copy was finished).
>
>The older copies are equivalent to the fossil DNA of extinct species
>that we are getting information from. Not only is the older edition a
>fossil but it can be the missing link the actual ancestral species that
>we are unlikely to find in the fossil record.

It occurred to me that a reasonably accurate analogy, and one which
T.O. poster can easily relate to, is how Usenet topics branch from a
single OP into multiple and distinctive threads.

[RonO]

Except that you have to deal with the rampant snipping of parts and loss
of information. What we have to do with real organisms is to look at
the parts that they all share, and a branching thread doesn't often
share much in common with the original. How many side threads contain
the original post?

Ron Okimoto

[Robert Carnegie]

The "Christian Science" religion for instance objects
to treating cancer by methods other than praying, but
that isn't precisely about the cancer's right to life.

It's possible to keep cancer cells alive in a laboratory
long after the rest of their original owner has died,
but most of us would prefer the other way around.

A typical human contains more bacteria cells and bacteria
genes than human ones, such as a lively and complicated
society in your gut. So you have to wonder who is in charge.

[jillery]

The human body is an autocracy. Human genes hang onto an outdated
imperialist dogma which perpetuates the economic and social
differences in society, in which the working classes suffer the
violence inherent in the system.